Align RhaQ (characterized, see rationale)
to candidate GFF2762 PGA1_c28050 putative sugar transport system, permease protein
Query= uniprot:Q7BSH2 (337 letters) >FitnessBrowser__Phaeo:GFF2762 Length = 353 Score = 145 bits (367), Expect = 1e-39 Identities = 96/312 (30%), Positives = 157/312 (50%), Gaps = 9/312 (2%) Query: 30 VLLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLVISGEIDLSVAAI 89 V L + + + VF L F + L+ ++A A +L++++ IDLSV AI Sbjct: 43 VPLIVLVLSVIVFGLLLGSKFFSPFALTLILQQVGIVGIVACAQSLVILTAGIDLSVGAI 102 Query: 90 IALASTAMGA-AVQIGIGTPGLVLIGIGTGLACGVFNGVLVSVLKLPSIVVTIGTMSLFR 148 + L+S MG + G+ V G+ G CG NG LV+ +KLP +VT+G + Sbjct: 103 MVLSSVVMGQFTFRYGLPPEVAVACGLICGTICGFINGWLVARMKLPPFIVTLGMWQIVL 162 Query: 149 GISYI-----VLGDQAYGKYPADFAYFGQGYVVW--VFSFEFVLFIVLAVLFAILLHATN 201 +++ + Q FG+ + VF++ + ++L VL A +L T Sbjct: 163 ASNFLYSANETIRSQTIAAEAPLLQLFGEKIKIGGAVFTYGVIFMVILVVLLAYVLRHTA 222 Query: 202 FGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTRPSIAQGWE 261 +GR VYA+G++ AA SG+ V RV +++L+G++ A + R+GS P+ Q Sbjct: 223 WGRHVYAVGDDPEAAELSGVKVTRVLISVYMLSGLICAFAGWAMIGRIGSVSPTSGQLAN 282 Query: 262 LEVVTMVVLGGISILGGFRHDRGVFVIAAFVMGLVTFGLGLLNLPGIVMSIFIGLLIIVT 321 +E +T VV+GGIS+ GG G F A ++G+ T GL LL + IGLLII Sbjct: 283 IESITAVVIGGISLFGGRGSILGTF-FGALIVGVFTLGLRLLGADAQWTYLLIGLLIIAA 341 Query: 322 IAIPIIARRIKL 333 +A+ R++ + Sbjct: 342 VAVDQWIRKVSV 353 Lambda K H 0.330 0.145 0.423 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 355 Number of extensions: 27 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 337 Length of database: 353 Length adjustment: 29 Effective length of query: 308 Effective length of database: 324 Effective search space: 99792 Effective search space used: 99792 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory